Weighted single-step GWAS identifies genes influencing fillet color in rainbow trout

Authors: AHMED, RIDWAN - University Of Maryland; ALI, ALI - University Of Maryland; AL-TOBASEI, RAFET - Middle Tennessee State University; Leeds, Timothy - Tim; KENNEY, BRETT - University Of Maryland; SALEM, MOHAMED - University Of Maryland

Submitted to: Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/23/2022
Publication Date: 7/26/2022
Citation: Ahmed, R.O., Ali, A., Al-Tobasei, R., Leeds, T.D., Kenney, B., Salem, M. 2022. Weighted single-step GWAS identifies genes influencing fillet color in rainbow trout. Genes. 13(8),1331. https://doi.org/10.3390/genes13081331.
DOI: https://doi.org/10.3390/genes13081331

Interpretive Summary: The color of rainbow trout fillets affects consumer preference. Fillet color can be readily manipulated by adding astaxanthin (a natural pigment) to the diet, but its inclusion increases feed costs. Previous studies have demonstrated that fillet color is a heritable trait that can be improved via selective breeding. However, traditional selective breeding to improve fillet color is challenging because the trait cannot be measured directly on selection candidates and thus has received little attention. This study used a 50,000 single nucleotide polymorphism (SNP) chip to identify genomic regions affecting variation in fillet color. Results suggest that fillet color is a complex trait regulated by many genes involved in carotenoid metabolism, myoglobin homeostasis, protection against lipid oxidation, and maintenance of muscle structural integrity. This study furthers our understanding of the genetic architecture underlying variation in fillet color and may inform more efficient and effective genomic selection approaches to improve fillet color in rainbow trout populations.

Technical Abstract: The visual appearance of the fish fillet plays a role in determining consumer purchase decisions. Depending on the fish diet, a uniform bright white or reddish/pink color of rainbow trout fillet is desirable. Factors affecting fillet color are complex ranging from the ability of the live fish to accumulate carotenoids in the muscle, preharvest environmental conditions, muscle-to-fillet conversion processes, and storage conditions. Identifying genetic markers of fillet color is a desirable but challenging task for the aquaculture industry. This study used weighted single-step GWAS to explore the genetic basis of variability in fillet color parameters in rainbow trout fish. We identified several SNP windows explaining up to 3.5%, 2.5%, and 1.6% of the additive genetic variance for fillet redness, yellowness, and whiteness, respectively. SNPs are located within genes implicated in carotenoid metabolism (Beta, beta-carotene 15,15'-dioxygenase, retinol dehydrogenase) and myoglobin homeostasis (ATP synthase subunit beta, mitochondrial (ATP5F1B)). The above genes are involved in processes that influence muscle pigmentation in live and post-mortem flesh coloration. Other identified genes are involved in the maintenance of muscle structural integrity (kelch protein 41b (klh41b), collagen alpha-1(XXVIII) chain (COL28A1), and cathepsin K (CTSK)) and protection against lipid oxidation (peroxiredoxin, superoxide dismutase 2 (SOD2), sestrin-1, Ubiquitin carboxyl-terminal hydrolase-10 (USP10)). A-to-G single nucleotide polymorphism in Beta, beta-carotene 15,15'-dioxygenase, and USP10 result in isoleucine-to-valine and proline-to-leucine non-synonymous amino acid substitutions, respectively. Our results suggest that fillet color is a complex trait regulated by many genes involved in carotenoid metabolism, myoglobin homeostasis, protection against lipid oxidation and maintenance of muscle structural integrity. The significant SNPs identified in this study could be prioritized via genomic selection in breeding programs to improve fillet color in rainbow trout.